Überlandstrasse 133
P.O.Box 611
8600 Dübendorf

Ph. +41 (0)58 765 55 11
Fax +41 (0)58 765 50 28
Research » Phytoplankton » Projects
Eawag - Aquatic Research
  Home Contact Search DE | EN | FR
Phytoplankton Diversity - Francesco Pomati


The importance of microscale plankton dynamics for aquatic ecosystem functioning

Individual level diversity in traits and small-scale spatial and temporal heterogeneity are common features of aquatic microbial environments, but they are the hardest to measure drivers of biodiversity changes and plankton productivity.

We are developing innovative approaches to phytoplankton and lake-ecosystem monitoring and integrating data with community and ecosystem theory. The long-term goal is a correct understanding of plankton-driven ecosystem processes with the aim of contributing to a sustainable management of water resources, the biodiversity that they harbour and the services that they provide.


With the aim of detecting and understanding high frequency patterns in phytoplankton community dynamics, we have designed a lake monitoring platform (Aquaprobe) for the characterisation and counting of algal cells (scanning flow-cytometry), coupled with measurement of the physical water environment (multiparameter probe) and contingent meteorological conditions. The aim of this system, currently deployed in Lake Greifensee, is to automatically and with high frequency acquire information on meteorological conditions, phytoplankton composition, diversity, abundance, phytoplankton functional traits, water physico-chemical parameters, and to monitor these parameters over the vertical profile of the water column.

The first step towards understanding the causes and consequences of plankton biodiversity relies on the detection of detailed filed patterns of community dynamics, which can be the outcome of four processes: selection, drift, evolution and dispersal. Modelling and prediction strictly depend upon our ability to discern deterministic from purely stochastic processes acting on the standing trait diversity, and their consequences for community dynamics at different spatial and temporal scales. In this context, besides high-resolution monitoring data, we are exploring long-term datasets from European lakes to assess how important are regional processes (e.g. climatic changes and dispersal) versus local conditions (e.g. trophic state) in determining the assembly of local phytoplankton communities. Sampling on Lake Lucerne

Aided with dedicated statistical tests and computer simulations, we aim at describing the relationship between environmental changes, phytoplankton biodiversity, community dynamics and aquatic ecosystem process like the production or transfer of organic matter.

Development of individual trait-based approaches to phytoplankton biodiversity

What is the relationship between changes at the level of individuals, community dynamics and ecosystem processes (including productivity)? To address this question we focus on the development and application of trait-based approaches to understand how individual responses scale to higher-level effects.

We aim at describing single organisms based on expressed phenotypic traits that directly respond (response-traits) to environmental changes, disturbance, pollution as well as eco-evolutionary processes like selection, competition or predation. We want to derive indices of trait-diversity based on individually acquired data and determine trait-environment, trait-biodiversity and trait-productivity relationships.


We approach this challenge using scanning flow-cytometry and we have identified a set of focal phytoplankton traits that respond quickly and significantly to species interactions or environmental filters. Our results suggest that the description of functional diversity afforded by measured individual traits is extremely sensitive with regards to environmental change and tightly bound to productivity dynamics. Measures of biodiversity based on individual traits are important to understand the eco-evolutionary mechanisms that control diversity and functioning of natural communities, and may have a significant applied impact in the fields of biodiversity ecosystem-functioning and environmental risk assessment. We are also developing new clustering approaches for flow-cytometry data.

In-situ Sensing Tools for Understanding Rapid Microscale Plankton Dynamics

Aquaprobe on Lake Greifensee

In close collaboration with Eric Bakker and Bernhard Wehrli, we aim at developing new sensing tools to detect chemical gradients at high spatial and temporal resolution in the field in order to understand plankton biodiversity and productivity dynamics and their impacts on the local carbon cycle. This project will provide new tools to interrogate plankton microenvironments in situ and evaluate the ecosystem implications of microscale gradients and rapid biodiversity dynamics.

A suit of novel sensors for macronutrients, micronutrients, and physicochemical parameters will be tested in the lab, validated, then deployed in the field and used in tandem with scanning flow-cytometry in the automated monitoring platform Aquaprobe. This new set-up will feature on-line analysis of nutrients, micronutrients, and other chemical parameters relevant to the carbon cycle. Development of new chemical sensor technology will allow to directly target key ecological questions: 1) Which variables influence short-term fluctuations in phytoplankton dynamics triggering cyanobacterial blooms? 2) How do such occurrences affect the local carbon cycle?

The role of toxigenicity in the development of cyanobacterial blooms

The ecological role of cyanobacterial toxins is not well understood. Cyanotoxins encompass a wide variety of chemical structures and biological effects, with potential functions linked to cellular defence or physiological support for homeostatic mechanisms. We want to understand the environmental selection favouring toxic strains over non-toxic congeners, and the implications that toxin production has for food-web and ecosystem dynamics.

Assessing impacts of cyanobacterial blooms on aquatic environments in the context of climate change and nutrient pollution

The goal of this research project, funded in collaboration with Piet Spaak and Cristina Sandu (Romanian Academy of Science), is to reconstruct the history of cyanobacterial blooms and the occurrence of toxic genes from lake sediments. We aim at studying the regional dispersal patterns of cyanobacteria, and to understand the correlation between community structure, toxigenicity, blooms, and rearrangements (evolution) of toxic genes as a consequence of environmental changes.

Phytoplankton Knowledge about this history is crucial to understand cyanobacterial bloom drivers, predict the risk for harmful cyanobacterial blooms in the context of environmental change and their consequences for lake food webs. The formerly hyper-eutrophied Lake Greifensee, Switzerland, is an ideal study site to develop the method to reconstruct cyanobacterial blooms from sediment cores. Eventually, we want to apply the method to lakes of the Danube Delta.

Besides, we are also interested at assessing the effects of cyanobacteria on locally adapted zooplankton.

Multiple anthropogenic stressors and the resilience of natural communities 

Multiple human-induced stressors in the form of chemical pollutants, habitat transformation and climate change are affecting the structure, functioning and resilience of natural populations and communities. Interaction of multiple stressors occurs over a nested set of adaptive systems that span from cells to food-webs, and resilience is mediated by physiological, ecological and evolutionary responses at different spatial and temporal scales.

Our goal is to understand how environmentally relevant exposure scenarios to water-borne micropollutants affect these nested responses within plankton communities, interfere with the processes that maintain biodiversity and functioning of natural systems, impair the ability of communities to adapt to environmental gradients or additional stressors.

Key innovative aspects of our approach include the use of environmentally relevant scenarios and exposure levels, the targeting of multiple endpoints at increasing levels of biological complexity, and the use of data acquired at the individual level.

Interactions between Environmental Gradients and Emerging Pollutants in Natural Phytoplankton Communities

Sampling Lakes globally contribute to the cycle of nutrients, carbon and green-house gases and are generally among the first ecosystems to encounter novel pollutants of human origin as a consequence of discharge form industrial, urban and agricultural settlements. The final impact of these toxic mixtures on lake ecosystems is not well understood. The analysis of risk and effect require new approaches which must consider realistic environmental scenarios, which can potentially help disentangling the effects of a fluctuating environment from the effects of pollutants (multiple stressors).

Emerging contaminants such as pharmaceuticals and personal care products pose new concerns for the protection of water, and the assessment of risks associated with water-born drugs requires realistic exposure levels and a mixture toxicology approach. We want to understand the two-way interaction between natural changes in the planktonic environment and emerging micropollutants on biodiversity and productivity. We assess the effects of diversity levels on community resilience to stress and the effects of pollutants and changes in the growth environment on community structural and functional properties. In collaboration with Luca Nizzetto, we aim at exposing phytoplankton in their natural environment to emerging chemical stressors using novel field methods, for an assessment of the community adaptive capacity and resilience.

Pollution induced evolutionary responses in phytoplankton populations

Natural populations may evolve resistance to pollutants or their mixtures but how these toxic mixtures relate to the evolution of resistance traits and associated fitness costs is not well understood. Here we want to study how phytoplankton populations adapt to the “chemical world”. We interested in the number of generations and the levels of exposure that determine evolutionary adaptation to pollutants, how organisms genetically adapt, and what are the implications of evolved resistance for community dynamics and ecosystem functioning (for example primary production). Questions include: do realistic environmental levels of exposure to micropollutants induce individual responses as phenotypic plasticity?

How long phenotypic plasticity is maintained across generations? How long before phenotypic changes are fixed within populations under chemicals' selective pressure? In this project we attempt to experimentally evolve resistant phytoplankton strains (particularly cyanobacteria) by exposing them to water borne micropollutants in the laboratory. We focus several aspects that are of key importance to understand the evolutionary ecology of micropollutants exposure.

Metabolism of polar organic xenobiotics in phytoplankton

The fate, cycle and dynamics of micropollutants can be affected by phytoplankton diversity and growth dynamics. Knowledge on the importance of biotransformation of polar organic compounds in organisms of the aquatic food web is essential to mechanistically link environmental exposure with toxic effects but currently rather limited.

Samples The metabolic profiles, the enzymatic activities involved and the identity of transformation products are not known in most cases although this is necessary to determine whether the metabolism results in bioactivation or detoxification of xenobiotics. This is important for scientific derivation of environmental quality standards in the context of the water framework directive as well as the evaluation of the bioaccumulation potential for registration of new chemicals within REACH.

This project is funded in collaboration with Juliane Hollender and aims at characterising the biotransformation of polar compounds in aquatic invertebrates and determining the importance for bioaccumulation as well as the contribution to fate in the aquatic environment. Specifically, here we are interested in to what extent the bioaccumulation and biotransformation in algal communities contributes to the fate in the aquatic environment, and how important is the role of biodiversity in the compounds’ environmental persistence

The Laboratory website is always under construction, for more information please contact Francesco Pomati.



Department Aquatic Ecology

Überlandstrasse 133
P.O. Box 611
8600 Dübendorf

Ph. +41 (0)58 765 5132
Fax +41 (0)58 765 5315